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Giussani B, Gorla G, Riu J. Analytical Chemistry Strategies in the Use of Miniaturised NIR Instruments: An Overview. Crit Rev Anal Chem 2024; 54:11-43. [PMID: 35286178 DOI: 10.1080/10408347.2022.2047607] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Miniaturized NIR instruments have been increasingly used in the last years, and they have become useful tools for many applications on a broad variety of samples. This review focuses on miniaturized NIR instruments from an analytical point of view, to give an overview of the analytical strategies used in order to help the reader to set up their own analytical methods, from the sampling to the data analysis. It highlights the uses of these instruments, providing a critical discussion including current and future trends.
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Affiliation(s)
- Barbara Giussani
- Dipartimento di Scienza e Alta Tecnologia, Università degli Studi dell'Insubria, Como, Italy
| | - Giulia Gorla
- Dipartimento di Scienza e Alta Tecnologia, Università degli Studi dell'Insubria, Como, Italy
| | - Jordi Riu
- Department of Analytical Chemistry and Organic Chemistry, Universitat Rovira i Virgili, Tarragona, Spain
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Kristoffersen KA, Måge I, Wubshet SG, Böcker U, Riiser Dankel K, Lislelid A, Rønningen MA, Afseth NK. FTIR-based prediction of collagen content in hydrolyzed protein samples. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 301:122919. [PMID: 37295376 DOI: 10.1016/j.saa.2023.122919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 05/04/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023]
Abstract
Fourier transform infrared spectroscopy (FTIR) is a powerful analytical tool that has been used for protein and peptide characterization for decades. In the present study, the objective was to investigate if FTIR can be used to predict collagen content in hydrolyzed protein samples. All samples were obtained from enzymatic protein hydrolysis (EPH) of poultry by-products providing a span in collagen content from 0.3% to 37.9% (dry weight), and the FTIR analysis was performed using dry film FTIR. Since nonlinear effects were revealed by calibration using standard partial least squares (PLS) regression, Hierarchical Cluster-based PLS (HC-PLS) calibration models were constructed. The HC-PLS model provided a low prediction error when validated using an independent test set (RMSE = 3.3% collagen), while validation using real industrial samples also showed satisfying results (RMSE = 3.2%). The results corresponded well with previously published FTIR-based studies of collagen, and characteristic spectral features for collagen were well identified in the regression models. Covariance between collagen content and other EPH related processing parameters could also be ruled out in the regression models. To the authors' knowledge, this is the first time that collagen content has been systematically studied in solutions of hydrolysed proteins using FTIR. This is also one of few examples where FTIR is successfully used to quantify protein composition. The dry-film FTIR approach presented in the study is expected to be an important tool in the growing industrial segment that is based on sustainable utilization of collagen-rich biomass.
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Affiliation(s)
- Kenneth Aase Kristoffersen
- Nofima AS - Norwegian Institute of Food, Fisheries and Aquaculture Research, PB 210, NO-1431 Ås, Norway; Faculty of Chemistry, Biotechnology, and Food Science, NMBU - Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway
| | - Ingrid Måge
- Nofima AS - Norwegian Institute of Food, Fisheries and Aquaculture Research, PB 210, NO-1431 Ås, Norway
| | - Sileshi Gizachew Wubshet
- Nofima AS - Norwegian Institute of Food, Fisheries and Aquaculture Research, PB 210, NO-1431 Ås, Norway
| | - Ulrike Böcker
- Nofima AS - Norwegian Institute of Food, Fisheries and Aquaculture Research, PB 210, NO-1431 Ås, Norway
| | - Katinka Riiser Dankel
- Nofima AS - Norwegian Institute of Food, Fisheries and Aquaculture Research, PB 210, NO-1431 Ås, Norway
| | - Andreas Lislelid
- Nofima AS - Norwegian Institute of Food, Fisheries and Aquaculture Research, PB 210, NO-1431 Ås, Norway; Department of Mechanical, Electronics and Chemical Engineering, Faculty of Technology, Art and Design, OsloMet - Oslo Metropolitan University, P.O. Box 4, St. Olavs plass, NO-0130 Oslo, Norway
| | - Mats Aksnes Rønningen
- Nofima AS - Norwegian Institute of Food, Fisheries and Aquaculture Research, PB 210, NO-1431 Ås, Norway; Department of Mechanical, Electronics and Chemical Engineering, Faculty of Technology, Art and Design, OsloMet - Oslo Metropolitan University, P.O. Box 4, St. Olavs plass, NO-0130 Oslo, Norway
| | - Nils Kristian Afseth
- Nofima AS - Norwegian Institute of Food, Fisheries and Aquaculture Research, PB 210, NO-1431 Ås, Norway.
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FRANZOI M, COSTA A, VIGOLO V, PENASA M, DE MARCHI M. Effect of pasteurization on coagulation properties of bovine milk and the role of major composition traits and protein fractions. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2022.104808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Raman and near Infrared Spectroscopy for Quantification of Fatty Acids in Muscle Tissue—A Salmon Case Study. Foods 2022; 11:foods11070962. [PMID: 35407049 PMCID: PMC8997921 DOI: 10.3390/foods11070962] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/18/2022] [Accepted: 03/22/2022] [Indexed: 01/27/2023] Open
Abstract
The aim of the present study was to critically evaluate the potential of using NIR and Raman spectroscopy for prediction of fatty acid features and single fatty acids in salmon muscle. The study was based on 618 homogenized salmon muscle samples acquired from Atlantic salmon representing a one year-class nucleus, fed the same high fish oil feed. NIR and Raman spectra were used to make regression models for fatty acid features and single fatty acids measured by gas chromatography. The predictive performance of both NIR and Raman was good for most fatty acids, with R2 above 0.6. Overall, Raman performed marginally better than NIR, and since the Raman models generally required fewer components than respective NIR models to reach high and optimal performance, Raman is likely more robust for measuring fatty acids compared to NIR. The fatty acids of the salmon samples co-varied to a large extent, a feature that was exacerbated by the overlapping peaks in NIR and Raman spectra. Thus, the fatty acid related variation of the spectroscopic data of the present study can be explained by only a few independent principal components. For the Raman spectra, this variation was dominated by functional groups originating from long-chain polyunsaturated FAs like EPA and DHA. By exploring the independent EPA and DHA Raman models, spectral signatures similar to the respective pure fatty acids could be seen. This proves the potential of Raman spectroscopy for single fatty acid prediction in muscle tissue.
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Skou PB, Hosseini E, Ghasemi JB, Smilde AK, Eskildsen CE. Orthogonality constrained inverse regression to improve model selectivity and analyte predictions from vibrational spectroscopic measurements. Anal Chim Acta 2021; 1185:339073. [PMID: 34711318 DOI: 10.1016/j.aca.2021.339073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 11/29/2022]
Abstract
In analytical chemistry spectroscopy is attractive for high-throughput quantification, which often relies on inverse regression, like partial least squares regression. Due to a multivariate nature of spectroscopic measurements an analyte can be quantified in presence of interferences. However, if the model is not fully selective against interferences, analyte predictions may be biased. The degree of model selectivity against an interferent is defined by the inner relation between the regression vector and the pure interfering signal. If the regression vector is orthogonal to the signal, this inner relation equals zero and the model is fully selective. The degree of model selectivity largely depends on calibration data quality. Strong correlations may deteriorate calibration data resulting in poorly selective models. We show this using a fructose-maltose model system. Furthermore, we modify the NIPALS algorithm to improve model selectivity when calibration data are deteriorated. This modification is done by incorporating a projection matrix into the algorithm, which constrains regression vector estimation to the null-space of known interfering signals. This way known interfering signals are handled, while unknown signals are accounted for by latent variables. We test the modified algorithm and compare it to the conventional NIPALS algorithm using both simulated and industrial process data. The industrial process data consist of mid-infrared measurements obtained on mixtures of beta-lactoglobulin (analyte of interest), and alpha-lactalbumin and caseinoglycomacropeptide (interfering species). The root mean squared error of beta-lactoglobulin (% w/w) predictions of a test set was 0.92 and 0.33 when applying the conventional and the modified NIPALS algorithm, respectively. Our modification of the algorithm returns simpler models with improved selectivity and analyte predictions. This paper shows how known interfering signals may be utilized in a direct fashion, while benefitting from a latent variable approach. The modified algorithm can be viewed as a fusion between ordinary least squares regression and partial least squares regression and may be very useful when knowledge of some (but not all) interfering species is available.
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Affiliation(s)
- Peter B Skou
- Arla Foods Ingredients Group P/S, DK-6920, Videbæk, Denmark
| | - Ensie Hosseini
- School of Chemistry, College of Science, University of Tehran, IR-1417614411, Tehran, Iran
| | - Jahan B Ghasemi
- School of Chemistry, College of Science, University of Tehran, IR-1417614411, Tehran, Iran
| | - Age K Smilde
- Swammerdam Institute for Life Sciences, University of Amsterdam, NL-1098 XH, Amsterdam, the Netherlands
| | - Carl Emil Eskildsen
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, NL-1098 XH, Amsterdam, the Netherlands.
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Bresolin T, Dórea JRR. Infrared Spectrometry as a High-Throughput Phenotyping Technology to Predict Complex Traits in Livestock Systems. Front Genet 2020; 11:923. [PMID: 32973876 PMCID: PMC7468402 DOI: 10.3389/fgene.2020.00923] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/24/2020] [Indexed: 12/17/2022] Open
Abstract
High-throughput phenotyping technologies are growing in importance in livestock systems due to their ability to generate real-time, non-invasive, and accurate animal-level information. Collecting such individual-level information can generate novel traits and potentially improve animal selection and management decisions in livestock operations. One of the most relevant tools used in the dairy and beef industry to predict complex traits is infrared spectrometry, which is based on the analysis of the interaction between electromagnetic radiation and matter. The infrared electromagnetic radiation spans an enormous range of wavelengths and frequencies known as the electromagnetic spectrum. The spectrum is divided into different regions, with near- and mid-infrared regions being the main spectral regions used in livestock applications. The advantage of using infrared spectrometry includes speed, non-destructive measurement, and great potential for on-line analysis. This paper aims to review the use of mid- and near-infrared spectrometry techniques as tools to predict complex dairy and beef phenotypes, such as milk composition, feed efficiency, methane emission, fertility, energy balance, health status, and meat quality traits. Although several research studies have used these technologies to predict a wide range of phenotypes, most of them are based on Partial Least Squares (PLS) and did not considered other machine learning (ML) techniques to improve prediction quality. Therefore, we will discuss the role of analytical methods employed on spectral data to improve the predictive ability for complex traits in livestock operations. Furthermore, we will discuss different approaches to reduce data dimensionality and the impact of validation strategies on predictive quality.
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Affiliation(s)
- Tiago Bresolin
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - João R R Dórea
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
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Zaalberg RM, Buitenhuis AJ, Sundekilde UK, Poulsen NA, Bovenhuis H. Genetic analysis of orotic acid predicted with Fourier transform infrared milk spectra. J Dairy Sci 2020; 103:3334-3348. [PMID: 32008779 DOI: 10.3168/jds.2018-16057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 12/03/2019] [Indexed: 01/08/2023]
Abstract
Fourier transform infrared spectral analysis is a cheap and fast method to predict milk composition. A not very well studied milk component is orotic acid. Orotic acid is an intermediate in the biosynthesis pathway of pyrimidine nucleotides and is an indicator for the metabolic cattle disorder deficiency of uridine monophosphate synthase. The function of orotic acid in milk and its effect on calf health, health of humans consuming milk or milk products, manufacturing properties of milk, and its potential as an indicator trait are largely unknown. The aims of this study were to determine if milk orotic acid can be predicted from infrared milk spectra and to perform a large-scale phenotypic and genetic analysis of infrared-predicted milk orotic acid. An infrared prediction model for orotic acid was built using a training population of 292 Danish Holstein and 299 Danish Jersey cows, and a validation population of 381 Danish Holstein cows. Milk orotic acid concentration was determined with nuclear magnetic resonance spectroscopy. For genetic analysis of infrared orotic acid, 3 study populations were used: 3,210 Danish Holstein cows, 3,360 Danish Jersey cows, and 1,349 Dutch Holstein Friesian cows. Using partial least square regression, a prediction model for orotic acid was built with 18 latent variables. The error of the prediction for the infrared model varied from 1.0 to 3.2 mg/L, and the accuracy varied from 0.68 to 0.86. Heritability of infrared orotic acid predicted with the standardized prediction model was 0.18 for Danish Holstein, 0.09 for Danish Jersey, and 0.37 for Dutch Holstein Friesian. We conclude that milk orotic acid can be predicted with moderate to good accuracy based on infrared milk spectra and that infrared-predicted orotic acid is heritable. The availability of a cheap and fast method to predict milk orotic acid opens up possibilities to study the largely unknown functions of milk orotic acid.
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Affiliation(s)
- R M Zaalberg
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, DK-8830 Tjele, Denmark.
| | - A J Buitenhuis
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, DK-8830 Tjele, Denmark
| | - U K Sundekilde
- Department of Food Science, Aarhus University, Kirstinebjergvej 10, DK-5792 Årslev, Denmark
| | - N A Poulsen
- Department of Food Science, Aarhus University, Blichers Allé 20, PO Box 50, DK-8830 Tjele, Denmark
| | - H Bovenhuis
- Animal Breeding and Genomics, Wageningen University and Research, PO Box 338, 6700AH, Wageningen, the Netherlands
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Zaalberg RM, Janss L, Buitenhuis AJ. Genome-wide association study on Fourier transform infrared milk spectra for two Danish dairy cattle breeds. BMC Genet 2020; 21:9. [PMID: 32005101 PMCID: PMC6993354 DOI: 10.1186/s12863-020-0810-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 01/06/2020] [Indexed: 11/10/2022] Open
Abstract
Background Infrared spectral analysis of milk is cheap, fast, and accurate. Infrared light interacts with chemical bonds present inside the milk, which means that Fourier transform infrared milk spectra are a reflection of the chemical composition of milk. Heritability of Fourier transform infrared milk spectra has been analysed previously. Further genetic analysis of Fourier transform infrared milk spectra could give us a better insight in the genes underlying milk composition. Breed influences milk composition, yet not much is known about the effect of breed on Fourier transform infrared milk spectra. Improved understanding of the effect of breed on Fourier transform infrared milk spectra could enhance efficient application of Fourier transform infrared milk spectra. The aim of this study is to perform a genome wide association study on a selection of wavenumbers for Danish Holstein and Danish Jersey. This will improve our understanding of the genetics underlying milk composition in these two dairy cattle breeds. Results For each breed separately, fifteen wavenumbers were analysed. Overall, more quantitative trait loci were observed for Danish Jersey compared to Danish Holstein. For both breeds, the majority of the wavenumbers was most strongly associated to a genomic region on BTA 14 harbouring DGAT1. Furthermore, for both breeds most quantitative trait loci were observed for wavenumbers that interact with the chemical bond C-O. For Danish Jersey, wavenumbers that interact with C-H were associated to genes that are involved in fatty acid synthesis, such as AGPAT3, AGPAT6, PPARGC1A, SREBF1, and FADS1. For wavenumbers which interact with –OH, associations were observed to genomic regions that have been linked to alpha-lactalbumin. Conclusions The current study identified many quantitative trait loci that underlie Fourier transform infrared milk spectra, and thus milk composition. Differences were observed between groups of wavenumbers that interact with different chemical bonds. Both overlapping and different QTL were observed for Danish Holstein and Danish Jersey.
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Affiliation(s)
- R M Zaalberg
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, DK-8830, Tjele, Denmark.
| | - L Janss
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, DK-8830, Tjele, Denmark
| | - A J Buitenhuis
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, DK-8830, Tjele, Denmark
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El Jabri M, Sanchez MP, Trossat P, Laithier C, Wolf V, Grosperrin P, Beuvier E, Rolet-Répécaud O, Gavoye S, Gaüzère Y, Belysheva O, Notz E, Boichard D, Delacroix-Buchet A. Comparison of Bayesian and partial least squares regression methods for mid-infrared prediction of cheese-making properties in Montbéliarde cows. J Dairy Sci 2019; 102:6943-6958. [PMID: 31178172 DOI: 10.3168/jds.2019-16320] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/23/2019] [Indexed: 01/17/2023]
Abstract
Assessing the cheese-making properties (CMP) of milks with a rapid and cost-effective method is of particular interest for the Protected Designation of Origin cheese sector. The aims of this study were to evaluate the potential of mid-infrared (MIR) spectra to estimate coagulation and acidification properties, as well as curd yield (CY) traits of Montbéliarde cow milk. Samples from 250 cows were collected in 216 commercial herds in Franche-Comté with the objectives to maximize the genetic diversity as well as the variation in milk composition. All coagulation and CY traits showed high variability (10 to 43%). Reference analyses performed for soft (SC) and pressed cooked (PCC) cheese technology were matched with MIR spectra. Prediction models were built on 446 informative wavelengths not tainted by the water absorbance, using different approaches such as partial least squares (PLS), uninformative variable elimination PLS, random forest PLS, Bayes A, Bayes B, Bayes C, and Bayes RR. We assessed equation performances for a set of 20 CMP traits (coagulation: 5 for SC and 4 for PCC; acidification: 5 for SC and 3 for PCC; laboratory CY: 3) by comparing prediction accuracies based on cross-validation. Overall, variable selection before PLS did not significantly improve the performances of the PLS regression, the prediction differences between Bayesian methods were negligible, and PLS models always outperformed Bayesian models. This was likely a result of the prior use of informative wavelengths of the MIR spectra. The best accuracies were obtained for curd yields expressed in dry matter (CYDM) or fresh (CYFRESH) and for coagulation traits (curd firmness for PCC and SC) using the PLS regression. Prediction models of other CMP traits were moderately to poorly accurate. Whatever the prediction methodology, the best results were always obtained for CY traits, probably because these traits are closely related to milk composition. The CYDM predictions showed coefficient of determination (R2) values up to 0.92 and 0.87, and RSy,x values of 3 and 4% for PLS and Bayes regressions, respectively. Finally, we divided the data set into calibration (2/3) and validation (1/3) sets and developed prediction models in external validation using PLS regression only. In conclusion, we confirmed, in the validation set, an excellent prediction for CYDM [R2 = 0.91, ratio of performance to deviation (RPD) = 3.39] and a very good prediction for CYFRESH (R2 = 0.84, RPD = 2.49), adequate for analytical purposes. We also obtained good results for both PCC and SC curd firmness traits (R2 ≥ 0.70, RPD ≥1.8), which enable quantitative prediction.
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Affiliation(s)
- M El Jabri
- Institut de l'Elevage, F-75012 Paris, France.
| | - M-P Sanchez
- GABI, INRA, AgroParisTech, Université Paris-Saclay, F-78350 Jouy-en-Josas, France
| | | | - C Laithier
- Institut de l'Elevage, F-75012 Paris, France
| | - V Wolf
- Conseil Elevage 25-90, F-25640 Roulans, France
| | | | - E Beuvier
- URTAL, INRA, F-39800 Poligny, France
| | | | - S Gavoye
- ACTALIA, F-39800 Poligny, France
| | - Y Gaüzère
- Ecole Nationale d'Industrie Laitière et des Biotechnologies, F-39800 Poligny, France
| | - O Belysheva
- Ecole Nationale d'Industrie Laitière et des Biotechnologies, F-39800 Poligny, France
| | - E Notz
- Centre Technique des Fromages Comtois, F-39800 Poligny, France
| | - D Boichard
- GABI, INRA, AgroParisTech, Université Paris-Saclay, F-78350 Jouy-en-Josas, France
| | - A Delacroix-Buchet
- GABI, INRA, AgroParisTech, Université Paris-Saclay, F-78350 Jouy-en-Josas, France
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Su WH, Sun DW. Mid-infrared (MIR) Spectroscopy for Quality Analysis of Liquid Foods. FOOD ENGINEERING REVIEWS 2019. [DOI: 10.1007/s12393-019-09191-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Bonfatti V, Vicario D, Lugo A, Carnier P. Genetic parameters of measures and population-wide infrared predictions of 92 traits describing the fine composition and technological properties of milk in Italian Simmental cattle. J Dairy Sci 2017; 100:5526-5540. [DOI: 10.3168/jds.2016-11667] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 03/15/2017] [Indexed: 11/19/2022]
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